mppR (version 1.4.0)

plot_QTLxEC: plot QTLxEC effect

Description

Plot allowing the visualisation of the QTL allelic effect given an environmental covariate (EC). It represents parental QTL effects that significantly interact with the EC. Those values are added to the (central) reference parent effect (intercept) which allow a comparison of the parental allele contribution with respect to the reference and in the scale of the trait.

Usage

plot_QTLxEC(
  Qeff,
  Q_id,
  RP = "RP",
  EC_id = "EC",
  trait_id = "trait",
  main = "QTLxEC",
  keep_par = NULL,
  rem_par = NULL,
  text_size = 14
)

Value

QTLxEC sensitivity plot

Arguments

Qeff

output from the function QTL_effect_QxEC obtained with option QTLxEC_plot = TRUE.

Q_id

Numeric value indicating which QTL to plot

RP

Character string indicating the name of the reference (central) parent. Default = 'RP'.

EC_id

Character string indicating the name of the environmental covariate. Default = 'EC'.

trait_id

Character string indicating the name of the trait. Default = 'trait'.

main

Character string title of the plot. Default = 'QTLxEC'

keep_par

Character vector or string specifying the only parents that should be ploted. Default = NULL.

rem_par

Character vector or string specifying the parents that should not be ploted. Default = NULL.

text_size

Numerical value specifying the size of the text in the plot. Default = 14.

Author

Vincent Garin

Examples

if (FALSE) {

data(mppData_GE)

Qpos <- c("PZE.105068880", "PZE.106098900")

EC <- matrix(c(180, 310, 240, 280), 4, 1)
rownames(EC) <- c('CIAM', 'TUM', 'INRA', 'KWS')
colnames(EC) <- 'cum_rain'

Qeff <- QTL_effect_QxEC(mppData = mppData_GE,
                         trait = c('DMY_CIAM', 'DMY_TUM', 'DMY_INRA_P', 'DMY_KWS'),
                         env_id = c('CIAM', 'TUM', 'INRA', 'KWS'),
                         QTL = Qpos, EC = EC)

pl <- plot_QTLxEC(Qeff, Q_id = 2, RP = "UH007", EC_id = 'cum rain',
trait_id = 'DMY')

}